Evaluation of the commercially available LightMix® Modular E-gene kit using clinical and proficiency testing specimens for SARS-CoV-2 detection

Yip, Cyril Chik-Yan; Sridhar, Siddharth; Cheng, Andrew Kim-Wai; Leung, Kit-Hang; Choi, Garnet Kwan-Yue; Chen, Jonathan Hon-Kwan; Poon, Rosana Wing-Shan; Chan, Kwok-Hung; Wu, Alan Ka-Lun; Chan, Helen Shuk-Ying; Chau, Sandy Ka-Yee; Chung, Tom Wai-Hin; To, Kelvin Kai-Wang; Tsang, Owen Tak-Yin; Hung, Ivan Fan-Ngai; Cheng, Vincent Chi-Chung; Yuen, Kwok- Yung; Chan, Jasper Fuk-Woo

BACKGROUND: Rapid and sensitive diagnostic assays for SARS-CoV-2 detection are required for prompt patient management and infection control. The analytical and clinical performances of LightMix® Modular SARS and Wuhan CoV E-gene kit, a widely used commercial assay for SARS-CoV-2 detection, have not been well studied. OBJECTIVE: To evaluate the performance characteristics of the LightMix® E-gene kit in comparison with well-validated in-house developed tests. STUDY DESIGN: Serial dilutions of SARS-CoV-2 culture isolate extracts were used for analytical sensitivity evaluation. A total of 289 clinical specimens from 186 patients with suspected COVID-19 and 8 proficiency testing (PT) samples were used to evaluate the diagnostic performance of the LightMix® E-gene kit against in-house developed COVID-19-RdRp/Hel and COVID-19-N RT-PCR assays. RESULTS: The LightMix® E-gene kit had a limit-of-detection of 1.8 × 10(-1) TCID(50)/mL, which was one log(10) lower than those of the two in-house RT-PCR assays. The LightMix® E-gene kit (149/289 [51.6%]) had higher diagnostic sensitivity than the in-house assays (144/289 [49.8%] for RdRp/Hel and 146/289 [50.5%] for N). All three assays gave correct results for all the PT samples. Cycle threshold (Cp) values of the LightMix® E-gene kit and in-house assays showed excellent correlation. Reproducibility of the Cp values was satisfactory with intra- and inter-assay coefficient of variation values <5%. Importantly, the LightMix® E-gene kit, when used as a stand-alone assay, was equally sensitive as testing algorithms using multiple SARS-CoV-2 assays. CONCLUSIONS: The LightMix® E-gene kit is a rapid and sensitive assay for SARS-CoV-2 diagnostics, with fewer verification requirements compared to laboratory-developed tests